Soil-borne legacy facilitates the dissemination of antibiotic resistance genes in soil-plant continua

Abstract

Antimicrobial resistance (AMR) disseminates throughout the soil-plant continuum via complex microbial interactions. Plants shape root- and leaf-associated microbiomes that sustain plant health; however, soil-borne legacies-enriched with antibiotic-producing microbes and resistance genes-govern AMR dynamics across agroecosystems. Using 16S rRNA gene sequencing, shotgun metagenomics, and high-throughput quantitative PCR, we profiled antibiotic resistance genes (ARGs), mobile genetic elements, and virulence factor genes across bulk soil, rhizosphere, phyllosphere, and root endosphere within soil-tomato and soil-strawberry continua. Recurrent bacterial wilt amplified the resistome, particularly polypeptide resistance genes, thereby establishing the rhizosphere as a major hotspot of ARG accumulation. Multidrug-resistant Ralstonia solanacearum (R. solanacearum) strains acted as major ARG reservoirs, harboring resistance determinants on both chromosomes and megaplasmids. Collectively, these findings demonstrate that pathogen-driven restructuring of the plant microbiome accelerates ARG dissemination, establishing soil-borne diseases as critical amplifiers of AMR across agricultural ecosystems.

Figure 1

Soil‐borne legacies facilitate the dissemination of ARGs in soil–plant continua. (A) Experimental flowchart. The study consisted of four experiments: two field investigations and two confirmatory assays. In the first field study, the resistome and microbiome—including bacteria, ARGs, VFGs, MGEs, and metabolic pathways—were characterized in the soil–tomato continuum across diseased, healthy, and dying plants under field conditions. The second field study assessed the resistome in strawberry plants cultivated in the same soils following tomato harvest. In the first confirmatory assay, antibiotic resistance of R. solanacearum isolates was evaluated through sensitivity testing. In the second confirmatory assay, genomic analysis was conducted to identify ARGs in R. solanacearum isolates and to assess multidrug resistance. (B–D) Distribution and composition of the antibiotic resistome in the soil–tomato continuum across plant health states. Resistome composition is shown by type, with inner circles representing ARG subtypes and outer circles representing ARG types. Circle size indicates normalized ARG abundance in healthy (B), infected (C), and dead (D) groups. (E and F) Distribution, composition, and sources of ARGs in soil–strawberry continua across ecological niches. Resistome composition is illustrated with inner and outer circles representing ARG subtypes and types, respectively; circle size indicates normalized ARG abundance in CK (E) and TX (F) groups. (G) Source‐tracking analysis predicting the origins of ARGs in soil–strawberry continua across samples. NA, nutrient agar medium; HR, rhizosphere soil of healthy tomatoes; IR, rhizosphere soil of infected tomatoes; DR, rhizosphere soil of dead tomatoes; CK, soil–strawberry continuum from Tongxiang with no history of bacterial wilt; TX, soil–strawberry continuum from Tangxi with a history of bacterial wilt; TXF, strawberry fruits of TX; TXS, rhizosphere soil of TX.

Figure 2

Microbial hosts carrying ARGs, MGEs, and VFGs in soil–tomato and soil–strawberry continua. (A) Phylogenetic trees of MAGs from the soil–tomato (Upper left) and soil–strawberry (Lower left) continua, colored by ARG‐MGE, VFG‐MGE, ARG‐VFG‐MGE carriers, and others. (B) Representative contigs carrying ARG‐MGE clusters and their putative hosts in the soil–tomato continuum (NCBI best hits). (C) Representative contigs carrying ARG‐VFG clusters and their putative host (Escherichia coli) in the soil–tomato continuum. (D) Representative contigs carrying ARG‐MGE clusters and their putative hosts in the soil–strawberry continuum. The numerical values denote the starting positions of the genes. The red and black coloring corresponds to ARGs and other genes, respectively. Abbreviations: Tomato continuum – HR, rhizosphere of healthy plants; HE, root endosphere of healthy plants; HP, phyllosphere of healthy plants; IR, rhizosphere of infected plants; IE, root endosphere of infected plants; IP, phyllosphere of infected plants; DR, rhizosphere of dead plants; DE, root endosphere of dead plants; DP, phyllosphere of dead plants; InR, rhizosphere before disease onset. Strawberry continuum – CKF, fruits from disease‐free Tongxiang; CKS, rhizosphere soil from disease‐free Tongxiang; TXF, fruits from Tangxi; TXS, rhizosphere soil from Tangxi with bacterial wilt history.